On the Jabiim Escort quest there are two of the republic destroyers, I was able to get both command decks with my photon torpedoes. I went and scrolled back through and notice that it showed i only completed the quest once for it. Just wondering is this a bug or do you only get credit for one kill?

All bonus quests that require shielded targets(sommand decks and arrays at bottom of stations) can be done only once per day per mission. Not a bug.